Hello Bioconductor users,
I am playing around with ChipDb classes, in particular the illuminaHumanv4.db package. I am simply trying to create a table of annotations from that db using the select() method, as described in the help section.
I believe the only library needed to test this is
library("illuminaHumanv4.db")
The cols() function works fine
> cols(illuminaHumanv4.db)
[1] "PROBEID" "ENTREZID" "PFAM" "IPI" "PROSITE" "ACCNUM" "ALIAS" "CHR" "CHRLOC" "CHRLOCEND"
[11] "ENZYME" "MAP" "PATH" "PMID" "REFSEQ" "SYMBOL" "UNIGENE" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS"
[21] "GENENAME" "UNIPROT" "GO" "EVIDENCE" "ONTOLOGY" "GOALL" "EVIDENCEALL" "ONTOLOGYALL" "OMIM" "UCSCKG"
The keytypes() function works fine too
> keytypes(illuminaHumanv4.db)
[1] "ENTREZID" "PFAM" "IPI" "PROSITE" "ACCNUM" "ALIAS" "CHR" "CHRLOC" "CHRLOCEND" "ENZYME"
[11] "MAP" "PATH" "PMID" "REFSEQ" "SYMBOL" "UNIGENE" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS" "GENENAME"
[21] "UNIPROT" "GO" "EVIDENCE" "ONTOLOGY" "GOALL" "EVIDENCEALL" "ONTOLOGYALL" "PROBEID" "OMIM" "UCSCKG"
However, when I run the keys() function, I am getting the following error
> keys(illuminaHumanv4.db)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘keys’ for signature ‘"ChipDb"’
According to the documentation, the ChipDb class should inherit this function from the AnnotationDb class. This causes a error when I try to run the select() function, since one of the arguments to pass is generated by the keys() function.
I have updated my environment (R 3.0.1, bioconductor 2.12) and all my packages and here is my sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid splines parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] hgu95av2.db_2.9.0 BiocInstaller_1.10.2 gplots_2.11.3 KernSmooth_2.23-10 caTools_1.14 gdata_2.13.2
[7] gtools_3.0.0 hash_2.2.6 shiny_0.6.0 GO.db_2.9.0 illuminaHumanv4.db_1.18.0 org.Hs.eg.db_2.9.0
[13] RSQLite_0.11.4 DBI_0.2-7 annotate_1.38.0 AnnotationDbi_1.22.6 genefilter_1.42.0 WGCNA_1.27-1
[19] doParallel_1.0.3 iterators_1.0.6 foreach_1.4.1 MASS_7.3-27 reshape_0.8.4 plyr_1.8
[25] cluster_1.14.4 Hmisc_3.12-2 survival_2.37-4 flashClust_1.01-2 dynamicTreeCut_1.21 impute_1.34.0
[31] Biobase_2.20.1 BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] AnnotationForge_1.2.2 bitops_1.0-5 codetools_0.2-8 compiler_3.0.1 digest_0.6.3 httpuv_1.0.6.3 IRanges_1.18.2
[8] lattice_0.20-15 Rcpp_0.10.4 RJSONIO_1.0-3 stats4_3.0.1 tools_3.0.1 XML_3.95-0.2 xtable_1.7-1
Let me know if anyone has run in the same problem recently.
Thank you!
Related
I can't seem to manage to get the action button in shiny working. Nothing happens when i press "click me" and there is no error message.
Does anyone have a clue what might be wrong?
library(shiny)
ui <- fluidPage(
tags$head(tags$script(src = "message-handler.js")),
actionButton("do", "Click Me")
)
server <- function(input, output, session) {
observeEvent(input$do, {
session$sendCustomMessage(type = 'testmessage',
message = 'Thank you for clicking')
})
}
shinyApp(ui, server)
here is my session info:
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=Swedish_Sweden.1252 LC_CTYPE=Swedish_Sweden.1252 LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C LC_TIME=Swedish_Sweden.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_1.4.0.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 packrat_0.5.0 digest_0.6.27 later_1.1.0.1 mime_0.9 R6_2.5.0 xtable_1.8-4 jsonlite_1.7.2 magrittr_2.0.1
[10] rlang_0.4.10 promises_1.1.0 tools_3.6.3 httpuv_1.5.2 rsconnect_0.8.16 fastmap_1.0.1 compiler_3.6.3 htmltools_0.5.1.1
In my toy package, I have defined %+% operator as an alias to paste0(). Trying to reduce interference with other packages, I realized it the following way:
`%+%` <- function(...) UseMethod("%+%")
`%+%.character` <- paste0
`%+%.numeric` <- paste0
`%+%.default` <- function (arg1, arg2){
e <- parent.env(getEnvByName(.GlobalEnv,'package:mypackagename'));
if (exists('%+%', envir = e)) get('%+%',envir = e)(arg1,arg2);
}
i.e. I override it only for character and numeric arguments, otherwise it tries to find if the method was previously defined.
It was working just fine until recently when it started giving an error:
'a' %+% 'b'
# Error in UseMethod("%+%") :
# no applicable method for '%+%' applied to an object of class "character"
It only fails when called outside of the package. If I define a function within the package, it works correctly:
# testab2() is defined in R file as a part of the package:
testab2 <- function(inpA, inpB){
print (inpA %+% inpB)
}
# when called outside of the package:
testab2('a','b')
# ab
I am pretty sure I didn't change anything in my code, so I'm wondering if it could be caused by R update. What could have changed and how to make it work back?
P.S. getEnvByName() is my helper function that searches for an object in parent environments:
getEnvByName <- function(inpEnv=.GlobalEnv, lookFor){
e <- inpEnv;
while (environmentName(e) != 'R_EmptyEnv' & environmentName(e)!=lookFor) e <- parent.env(e);
if (environmentName(e) != lookFor) return(NULL);
return(e);
}
And the exporting was done by the following lines in the NAMESPACE file:
exportPattern("^[[:alpha:]]+")
exportPattern("%.*%")
export("%+%.default")
export("%+%.character")
P.P.S. sessionInfo:
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
system code page: 1251
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] vautils_0.1.1.105 magrittr_1.5 data.table_1.13.0
loaded via a namespace (and not attached):
[1] dplyr_1.0.2 crayon_1.3.4 grid_4.0.2 R6_2.4.1 lifecycle_0.2.0 gtable_0.3.0
[7] scales_1.1.1 ggplot2_3.3.2 pillar_1.4.6 rlang_0.4.7 rstudioapi_0.11 generics_0.0.2
[13] vctrs_0.3.4 ellipsis_0.3.1 tools_4.0.2 glue_1.4.2 purrr_0.3.4 munsell_0.5.0
[19] compiler_4.0.2 pkgconfig_2.0.3 colorspace_1.4-1 tidyselect_1.1.0 tibble_3.0.3
To export S3 methods, your NAMESPACE file needs to (in your case) contain the following declarations:
export(`%+%`)
S3method(`%+%`, default)
S3method(`%+%`, character)
S3method(`%+%`, numeric)
That is, export the %+% generic, and declare S3 methods for the methods.
Better yet, instead of manually editing the NAMESPACE file use ‘roxygen2’, which generates the correct declarations for you based on the #export documentation tag.
I've been trying to solve a problem with the RPostgreSQL package for quite some time. My code:
path_ene <- "C:/Users/omen03/ENE"
nene <- "ene_2010_02_efm.csv"
drv <- dbDriver("PostgreSQL")
con = dbConnect(drv, user="postgres", password="mypassword",
host="localhost", port=5432, dbname="ENE")
tn = "ene_2010_02_efm";
dbRemoveTable(con,tn);
dbWriteTable(conn = con, name = tn, value = paste0(path_ene,"/",nene),
sep = ",", overwrite = FALSE))
When executing the code described above, I throw the following error:
Error in postgresqlExecStatement (conn, statement, ...):
RS-DBI driver: (could not Retrieve the result: ERROR:
Could not open file «C: /Users/omen03/ENE/ene_2010_02_efm.csv» for reading: Permission denied
HINT: COPY FROM tells the PostgreSQL server process to read a
file. You may want to use a client-side facility such as psql \ copy.
) In addition: Warning message: In postgresqlImportFile (conn, name,
value, ...): could not load data into table
when I try without specifying the file path, it throws me another error
dbRemoveTable(con,tn);
dbWriteTable(conn = con, name = tn, value = nene),
sep = ",", overwrite = FALSE))
Error in postgresqlExecStatement (conn, statement, ...): RS-DBI
driver: (could not Retrieve the result: ERROR: could not open file Â
«./ ene_2010_02_efm» for reading: No such file or directory
HINT:
COPY FROM tells the PostgreSQL server process to read a file. You may
want to use a client-side facility such as psql \ copy. ) In addition:
Warning message: In postgresqlImportFile (conn, name, value, ...):
could not load data into table
Update:
Taking into account the error message, I decided to use sql directly to insert the csv values in each of the tables in the database. For that I used a couple of functions
createEmptyTable <- function(con,tn,df) {
sql <- paste0("create table \"",tn,"\" (",paste0(collapse=',','"',names(df),'" ',sapply(df[0,],postgresqlDataType)),");");
dbSendQuery(con,sql);
invisible();
};
Taken from: How to write a table in PostgreSQL from R?
and
#tn: Table name
#c_names: column names of each table (a list)
#source: The path to each csv files
insert_data = function(tn, source){
sql = paste0('COPY ',tn,' FROM \'',paste0(path_ene,'\\',source),'\' DELIMITER \',\' CSV HEADER')
dbSendQuery(con, sql);
}
insert_data(tn[1], paste0(path_ene, "/",nene[1]))
Anyway, I still get a very similar error.
Error in postgresqlExecStatement (conn, statement, ...): RS-DBI
driver: (could not Retrieve the result: ERROR: Could not open file Â
«C: /Users/omen03/ENE/ene_2010_02_efm.csv» for reading: Permission
denied HINT: COPY FROM tells the PostgreSQL server process to read a
file. You may want to use a client-side facility such as psql \ copy.
)
My session info:
R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)
Matrix products: default
locale: [1] LC_COLLATE=Spanish_Chile.1252 LC_CTYPE=Spanish_Chile.1252
LC_MONETARY=Spanish_Chile.1252 LC_NUMERIC=C [5]
LC_TIME=Spanish_Chile.1252
attached base packages: [1] stats graphics grDevices utils
datasets methods base
other attached packages: [1] RPostgreSQL_0.6-2 DBI_1.0.0
foreign_0.8-71 captioner_2.2.3 kableExtra_1.1.0 wordcloud_2.6
tidytext_0.2.2 gridExtra_2.3 [9] gtable_0.3.0
readstata13_0.9.2 RColorBrewer_1.1-2 ggrepel_0.8.1 pbapply_1.4-2
srvyr_0.3.6 data.table_1.12.6 lubridate_1.7.4 [17]
stringi_1.4.3 forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3
purrr_0.3.3 readr_1.3.1 tidyr_1.0.0 tibble_2.1.3
[25] ggplot2_3.2.1 tidyverse_1.3.0
loaded via a namespace (and not attached): [1] httr_1.4.1
jsonlite_1.6 viridisLite_0.3.0 splines_3.6.1 modelr_0.1.5
assertthat_0.2.1 cellranger_1.1.0 sessioninfo_1.1.1 [9]
pillar_1.4.3 backports_1.1.5 lattice_0.20-38 glue_1.3.1
digest_0.6.23 rvest_0.3.5 colorspace_1.4-1 htmltools_0.4.0
[17] Matrix_1.2-17 survey_3.36 pkgconfig_2.0.3 broom_0.5.2
haven_2.2.0 scales_1.1.0 webshot_0.5.2 generics_0.0.2
[25] withr_2.1.2 lazyeval_0.2.2 cli_2.0.0
survival_2.44-1.1 magrittr_1.5 crayon_1.3.4 readxl_1.3.1
evaluate_0.14 [33] tokenizers_0.2.1 janeaustenr_0.1.5 fs_1.3.1
fansi_0.4.0 nlme_3.1-140 SnowballC_0.6.0 xml2_1.2.2
tools_3.6.1 [41] hms_0.5.2 mitools_2.4
lifecycle_0.1.0 munsell_0.5.0 reprex_0.3.0 compiler_3.6.1
rlang_0.4.2 grid_3.6.1 [49] rstudioapi_0.10
rmarkdown_1.18 R6_2.4.1 knitr_1.26 zeallot_0.1.0
parallel_3.6.1 Rcpp_1.0.3 vctrs_0.2.1 [57]
dbplyr_1.4.2 tidyselect_0.2.5 xfun_0.11
Finally, I found the answer by looking for the problem of directly importing data into postgresql. It was enough to change the configuration of the folder containing the .csv files.
I reproduce this answer that was the one I finally used.
Right click the folder containing the data file(s) that permission was denied to and then click Properties.
In the Folder's Properties window, select the Security tab.
Click the Edit button. In the "Permissions for the folder" window that opened, click the Add... button.
Type Everyone into the "Enter the object names to select" text area box.
Click OK and the window will close.
I am not able to create a twitter token using create_token from rtweet package:
library (rtweet)
twitter_token <- create_token(app = appname, # as set in Twitter API
consumer_key = key, # as set in Twitter API
consumer_secret = secret) # as set in Twitter API
The output I get is:
Error in init_oauth1.0(self$endpoint, self$app, permission = self$params$permission, :
Forbidden (HTTP 403).
I followed the instructions to setup Twitter API as disclosed in http://rtweet.info/articles/auth.html, and triple checked that the Callback URL was properly set as http://127.0.0.1:1410.
I also tried:
createTokenNoBrowser<- function(appName, consumerKey, consumerSecret,
accessToken, accessTokenSecret) {
app <- httr::oauth_app(appName, consumerKey, consumerSecret)
params <- list(as_header = TRUE)
credentials <- list(oauth_token = accessToken,
oauth_token_secret = accessTokenSecret)
token <- httr::Token1.0$new(endpoint = NULL, params = params,
app = app, credentials = credentials)
return(token)
}
It seems to work, but when I call
rt <- stream_tweets(q = q, file_name = filename,token = twitter_token)
I get: Error: Not a valid access token.
What might be going wrong?
I am currently using R 3.5.0. Thank you.
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=Portuguese_Brazil.1252 LC_CTYPE=Portuguese_Brazil.1252 LC_MONETARY=Portuguese_Brazil.1252
[4] LC_NUMERIC=C LC_TIME=Portuguese_Brazil.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtweet_0.6.4
loaded via a namespace (and not attached):
[1] readr_1.1.1 httr_1.3.1 compiler_3.5.0 magrittr_1.5 R6_2.2.2 hms_0.4.2 tools_3.5.0 pillar_1.2.3
[9] curl_3.2 tibble_1.4.2 yaml_2.1.19 Rcpp_0.12.17 jsonlite_1.5 openssl_1.0.1 pkgconfig_2.0.1 rlang_0.2.1
This issue has been fixed in the newest version of rtweet on Github!
I believe create_token() is deprecated in the latest version of rtweet. Instead, you should use rtweet_app() or rtweet_bot().
I'm building a package but the documentation must be in Spanish, including the tilde character (i.e. í, é).
I have a simple function like this in an R file:
#' Función con acénto
#'
#' Permite instalar rápidamente de manera local un paquete previamente descargado
#' #param direccion La dirección del archivo local, poner .zip
#' #keywords FAhorroDS
#' #export
#' #encoding UTF-8
#' #author Eduardo Flores
#' #examples
#' FA_InstalarLocal("paquete_x_1.10.zip")
FA_InstalarLocal<-function(direccion)
{
install.packages(direccion, repos = NULL, type="source")
}
And building the Rd via devtools::document(). The Rd file in man generated seems fine:
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/test.R
\encoding{UTF-8}
\name{FA_InstalarLocal}
\alias{FA_InstalarLocal}
\title{Función con acénto}
\usage{
FA_InstalarLocal(direccion)
}
\arguments{
\item{direccion}{La dirección del archivo local, poner .zip}
}
\description{
Permite instalar rápidamente de manera local un paquete previamente descargado
}
\examples{
FA_InstalarLocal("paquete_x_1.10.zip")
}
\author{
Eduardo Flores
}
\keyword{FAhorroDS}
However even if i'm specifying the encoding both here and in the DOCUMENTATION file, when I run: system("R CMD Rd2pdf . --output=manual.pdf --force"), I get the following error:
Hmm ... looks like a package
Converting Rd files to LaTeX Warning: ./man/FA_InstalarLocal.Rd:6: Some input could not be re-encoded to ASCII
When I see the package, the description is okay, but the title of the function turns out as NA.
Any ideas as to why everything else (the description has a tilde) is being correctly encoded but not the title?
> sessionInfo()
R version 3.2.4 Revised (2016-03-16 r70336)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=Spanish_Mexico.1252 LC_CTYPE=Spanish_Mexico.1252
[3] LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C
[5] LC_TIME=Spanish_Mexico.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] fahorro_0.1 devtools_1.10.0 magrittr_1.5 readxl_0.1.0 dplyr_0.4.3
[6] FAhorroDS_1.0.1
loaded via a namespace (and not attached):
[1] Rcpp_0.11.6 roxygen2_5.0.1 R6_2.1.2 xlsx_0.5.7 stringr_1.0.0
[6] plyr_1.8.3 tools_3.2.4 parallel_3.2.4 DBI_0.3.1 withr_1.0.0
[11] assertthat_0.1 digest_0.6.9 rJava_0.9-8 RODBC_1.3-12 xlsxjars_0.6.1
[16] memoise_1.0.0 stringi_1.0-1 SOAR_0.99-11